Pathway Database System

The Case Western Reserve University s Pathways Database System [Ozsoyoglu, Nadeau, and Ozsoyoglu 2003] comes with a sample set of metabolic and signaling pathways, most drawn from Michal s Biochemical Pathways [Michal 1999], It consists of a suite of tools, including query interfaces, viewers, and a pathway editor. 

Ozsoyoglu, Z. M., J. Nadeau, and G. Ozsoyoglu. 2003. Pathways database system. OMICS 7 123-5, http //nashua.cwru.edu/pathways/... 

W. Xu, Bioinformatics, 22, 930 (2003). Pathways Database System An Int ated System for Biological Pathways. 

The reaction database compiled on Biochemical Pathways can be accessed on the web and can be investigated with the retrieval system C ROL (Compound Access and Retrieval On Line) [211 that provides a variety of powerful search techniques. The Biochemical Pathways database is split into a database of chemical structures and a database of chemical reactions that can be searched independently but which have been provided with efficient crosslinks between these two databases. 

For the metabolism of the molecule X (see Figure 10.5) used as in a recent comparison of several structure-metabolism relationship database systems (Wilbury, 1999), META produced the following pathways and rate priority numbers (in brackets) ... 

Identifying constraints on reaction directions is essential for applications of metabolic flux analysis. However, in many applications the procedure used for determining reaction directions is not concretely defined. Typically, a subset of the reactions in a model is assigned as irreversible and the feasible directions are assigned based on information in pathway databases [59], In these applications, by treating certain reactions as implicitly unidirectional, biologically reasonable results can often be obtained without considering the system thermodynamics as outlined above. 

For those who want to query PGDB data through a relational database system, the attribute-value files exported by Pathway Tools can be loaded into SRFs BioWarehouse system (14). BioWarehouse is an Oracle or MySQL-based system for integration of multiple public bioinformatics databases. PGDB data can be queried through BioWarehouse alone or in combination with other bioinformatics databases such as UniProt, Genbank, NCBI Taxonomy, ENZYME, and KEGG. 

The Remedial Action Priority System (RAPS) and Multimedia Environmental Pollutant Assessment System (MEPAS) are different names for an objective exposure pathway evaluation system developed by Pacific Northwest Laboratory to rank chemical and radioactive releases according to their potential human health impacts. Constituent migration and impact are simulated using air, groundwater, overland, surface water, and exposure components based on standard assessment principles and techniques. A shell allows interactive description of the environmental problem to be evaluated, defines required data in the form of problem-specific worksheets, and allows data input. The assessment methodology uses an extensive constituent database as a consistent source of chemical, physical, and health-related parameters. 

A discussion of the mathematical and computational tools already available for the analysis of GRN models is given in the next section. Most of the models extracted from pathways databases are expected to be qualitative and incomplete in nature hence, the discussion focuses on qualitative network structures and how these structures influence the capacity of the system to exhibit certain dynamical behavior. 

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